lumpy: drop
Removed because it requires python2 and the upstream repository looks undermaintained.
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@ -1,50 +0,0 @@
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{ lib, stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba
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, samtools, hexdump, python2Packages, which }:
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let
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python =
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python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]);
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in stdenv.mkDerivation rec {
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pname = "lumpy";
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version = "0.3.1";
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src = fetchFromGitHub {
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owner = "arq5x";
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repo = "lumpy-sv";
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rev = "v${version}";
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sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9";
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fetchSubmodules = true;
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};
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nativeBuildInputs = [ which ];
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buildInputs =
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[ htslib zlib curl openssl python samblaster sambamba samtools hexdump ];
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preConfigure = ''
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patchShebangs ./.
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# Use Nix htslib over bundled version
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sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
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sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
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# Also make sure we use the includes from Nix's htslib
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sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile
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'';
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# Upstream's makefile doesn't have an install target
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installPhase = ''
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mkdir -p $out
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cp -r bin $out
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cp -r scripts $out
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sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config
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'';
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meta = with lib; {
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description = "Probabilistic structural variant caller";
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homepage = "https://github.com/arq5x/lumpy-sv";
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maintainers = with maintainers; [ jbedo ];
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license = licenses.mit;
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platforms = [ "x86_64-linux" ];
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};
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}
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@ -568,6 +568,7 @@ mapAliases ({
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lua5_1_sockets = lua51Packages.luasocket; # added 2017-05-02
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lua5_expat = luaPackages.luaexpat; # added 2017-05-02
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lua5_sec = luaPackages.luasec; # added 2017-05-02
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lumpy = throw "lumpy has been removed from nixpkgs, as it is stuck on python2."; # added 2022-01-12
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lxappearance-gtk3 = throw "lxappearance-gtk3 has been removed. Use lxappearance instead, which now defaults to Gtk3"; # added 2020-06-03
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lzma = xz; # moved from top-level 2021-03-14
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m3d-linux = m33-linux; # added 2016-08-13
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@ -31669,8 +31669,6 @@ with pkgs;
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last = callPackage ../applications/science/biology/last { };
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lumpy = callPackage ../applications/science/biology/lumpy { };
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macse = callPackage ../applications/science/biology/macse { };
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MACS2 = callPackage ../applications/science/biology/MACS2 { };
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